Re: [ccp4bb] mysterious density
MES or HEPES, I reckon. Both of them can lose definition for the electron density in the morpolino/piperazine 6-membered ring due to flexibility between the ring and the sulphonic acid group when - leading to the tadpole-like density you describe. HTH, Dave -- Dr David C. Briggs CSci Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == Diamond User Group (DUC) MX representative == about.me/david_briggs From: CCP4 bulletin board on behalf of Xavier Brazzolotto Sent: 13 March 2022 17:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] mysterious density External Sender: Use caution. A MES buffer molecule ? > Le 13 mars 2022 à 18:08, doriano lamba a écrit : > > Glycerol-3-phosphate? > My 2cents > DL > Il 2022-03-13 15:19 Amir Khan ha scritto: >> Hi, >> I wonder whether anyone can advise on the ‘tadpole’ like density. >> The head is currently a phosphate >> and I’ve placed a water in tail, but it obviously looks connected… >> would appreciate any help! >> Green density at 5 sigma (Fo-fc), while blue is 2fo-fc at 1.3 sigma. >> Crystallization condition is unknown, though it came from sparse >> matrix commercial (either Wizard, Pact Prem, or JCSG+). >> Thanks! >> Amir >> - >> To unsubscribe from the CCP4BB list, click the following link: >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=GMEp7d3NUTKAFTwTTbDEBxMIvpjtlIikUsiGJ0BPOU4%3Dreserved=0 > > -- > Dr. Doriano Lamba > Scientific Associate - Retired Fellow > > Istituto di Cristallografia - C.N.R. > Sede Secondaria di Trieste > Area Science Park - Basovizza > Building Q1 - Room 106 > Strada Statale 14 - Km. 163.5 > I-34149 Trieste - Italy > > Mobile Phone: ++39 330411796 > Skype-name: doriano.lamba > E-mail: doriano.la...@ic.cnr.it > > ___ > WoS ResearchID: > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2961-2011data=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=A49X0X0K0b3MaJJKNb11fMAj%2BEjHfimVJE1PvjDK2MQ%3Dreserved=0 > ORCID ID: > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F-0001-6859-7868data=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=Mbn800FFWsZG0paCU69MtcJ2r4CuK4BzDvxzd627e08%3Dreserved=0 > Google Scholar: > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.it%2Fcitations%3Fhl%3Den%26user%3DYzLT5gUJ%26view_op%3Dlist_worksdata=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=yUYqI%2FNbMT4mCJFvQXoImX8zGggKaWqcExJxtfuzQpc%3Dreserved=0 > Research Gate: > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FDoriano_Lamba2data=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=Lf8RF535aB1ZvKm9WwR1KlUUGm2Pbk1cxtShLYTfuB8%3Dreserved=0 > Scopus ID: > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.scopus.com%2Fauthid%2Fdetail.url%3FauthorId%3D7003374970data=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=XTri3uAv3UqbTYj9w5mhK%2Bj1Mn6F8iFLxVievJssg1g%3Dreserved=0 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7C%7C7d385d0717a84b8e803f08da0516f581%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637827893421508121%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=GMEp7d3NUTKAFTwTTbDEBxMIvpjtlIikUsiGJ0BPOU4%3Dreserved=0 > > This message was issued to members of >
Re: [ccp4bb] mysterious density
A MES buffer molecule ? > Le 13 mars 2022 à 18:08, doriano lamba a écrit : > > Glycerol-3-phosphate? > My 2cents > DL > Il 2022-03-13 15:19 Amir Khan ha scritto: >> Hi, >> I wonder whether anyone can advise on the ‘tadpole’ like density. >> The head is currently a phosphate >> and I’ve placed a water in tail, but it obviously looks connected… >> would appreciate any help! >> Green density at 5 sigma (Fo-fc), while blue is 2fo-fc at 1.3 sigma. >> Crystallization condition is unknown, though it came from sparse >> matrix commercial (either Wizard, Pact Prem, or JCSG+). >> Thanks! >> Amir >> - >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- > Dr. Doriano Lamba > Scientific Associate - Retired Fellow > > Istituto di Cristallografia - C.N.R. > Sede Secondaria di Trieste > Area Science Park - Basovizza > Building Q1 - Room 106 > Strada Statale 14 - Km. 163.5 > I-34149 Trieste - Italy > > Mobile Phone: ++39 330411796 > Skype-name: doriano.lamba > E-mail: doriano.la...@ic.cnr.it > > ___ > WoS ResearchID: http://www.researcherid.com/rid/B-2961-2011 > ORCID ID: http://orcid.org/-0001-6859-7868 > Google Scholar: > https://scholar.google.it/citations?hl=en=YzLT5gUJ_op=list_works > Research Gate: https://www.researchgate.net/profile/Doriano_Lamba2 > Scopus ID: https://www.scopus.com/authid/detail.url?authorId=7003374970 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Adding hydrogens to a specific residue using Coot
On 13/03/2022 14:05, Tomas Malinauskas wrote: Dear All, Is it possible to add hydrogens to a specific residue using Coot? Something like Calculate -> Scripting -> Python -> coot_reduce(0) but targeting one residue only. sprout_hydrogens(0, "L", 101, "") # or some such: molecule-number chain-id res-no ins-code To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Adding hydrogens to a specific residue using Coot
Dear All, Is it possible to add hydrogens to a specific residue using Coot? Something like Calculate -> Scripting -> Python -> coot_reduce(0) but targeting one residue only. I thank you for your help. Best wishes, Tomas To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
